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1Y0G
Asym. Unit
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Asym.Unit (123 KB)
Biol.Unit 1 (60 KB)
Biol.Unit 2 (60 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI YCEI PROTEIN, STRUCTURAL GENOMICS
Authors
:
Y. V. Patskovsky, B. Strokopytov, U. Ramagopal, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date
:
15 Nov 04 (Deposition) - 21 Dec 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Lipid Binding Protein, Lipocalin, Cofactor, Coenzyme, Dehydrogenase, Hydrolase, Predicted, Structural Genomics, Protein Structure Initiative, Psi, Nysgxrc, New York Sgx Research Center For Structural Genomics
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
Y. V. Patskovsky, B. Strokopytov, U. Ramagopal, S. C. Almo
Crystal Structure Of The Escherichia Coli Ycei Periplasmic Protein
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: 2-[(2E,6E,10E,14E,18E,22E,26E)-3,7... (8PPa)
1b: 2-[(2E,6E,10E,14E,18E,22E,26E)-3,7... (8PPb)
1c: 2-[(2E,6E,10E,14E,18E,22E,26E)-3,7... (8PPc)
1d: 2-[(2E,6E,10E,14E,18E,22E,26E)-3,7... (8PPd)
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No.
Name
Count
Type
Full Name
1
8PP
4
Ligand/Ion
2-[(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL]PHENOL
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:36 , ILE A:40 , GLN A:41 , HIS A:42 , LEU A:48 , PHE A:52 , THR A:60 , LYS A:70 , VAL A:71 , VAL A:73 , ILE A:75 , ARG A:87 , PHE A:96 , ALA A:105 , PHE A:155 , ILE A:161 , LEU A:163 , LEU A:172 , ILE A:183 , VAL A:185 , HIS B:33
BINDING SITE FOR RESIDUE 8PP A 320
2
AC2
SOFTWARE
HIS A:33 , VAL B:36 , PHE B:38 , ILE B:40 , GLN B:41 , HIS B:42 , LEU B:48 , PHE B:52 , THR B:60 , PHE B:61 , LYS B:70 , VAL B:71 , VAL B:73 , ILE B:75 , ARG B:87 , LEU B:91 , ALA B:105 , PHE B:107 , PHE B:155 , ILE B:161 , LEU B:163 , ILE B:183 , VAL B:185 , GLY C:149
BINDING SITE FOR RESIDUE 8PP B 321
3
AC3
SOFTWARE
VAL C:36 , PHE C:38 , ILE C:40 , HIS C:42 , LEU C:48 , PHE C:52 , THR C:60 , LYS C:70 , VAL C:71 , VAL C:73 , ILE C:75 , ARG C:87 , LEU C:91 , ALA C:105 , PHE C:107 , PHE C:155 , ILE C:161 , LEU C:163 , ILE C:183 , VAL C:185 , HIS D:33
BINDING SITE FOR RESIDUE 8PP C 322
4
AC4
SOFTWARE
HIS C:33 , VAL D:36 , PHE D:38 , ILE D:40 , HIS D:42 , PHE D:52 , THR D:60 , PHE D:61 , ASP D:69 , LYS D:70 , VAL D:71 , VAL D:73 , ILE D:75 , LEU D:91 , ALA D:105 , PHE D:107 , LEU D:136 , PHE D:155 , ILE D:161 , LEU D:163 , LEU D:172 , ILE D:183 , VAL D:185 , HOH D:347
BINDING SITE FOR RESIDUE 8PP D 323
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1y0ga_ (A:)
1b: SCOP_d1y0gb_ (B:)
1c: SCOP_d1y0gc_ (C:)
1d: SCOP_d1y0gd_ (D:)
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Class
:
All beta proteins
(24004)
Fold
:
Streptavidin-like
(225)
Superfamily
:
YceI-like
(3)
Family
:
YceI-like
(2)
Protein domain
:
Lipid binding protein YceI
(1)
Escherichia coli [TaxId: 562]
(1)
1a
d1y0ga_
A:
1b
d1y0gb_
B:
1c
d1y0gc_
C:
1d
d1y0gd_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1y0gA00 (A:23-191)
1b: CATH_1y0gB00 (B:23-191)
1c: CATH_1y0gC00 (C:23-191)
1d: CATH_1y0gD00 (D:23-191)
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Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Lipocalin
(526)
Homologous Superfamily
:
Protein ycei
(2)
Escherichia coli. Organism_taxid: 562.
(1)
1a
1y0gA00
A:23-191
1b
1y0gB00
B:23-191
1c
1y0gC00
C:23-191
1d
1y0gD00
D:23-191
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_YceI_1y0gD01 (D:24-188)
1b: PFAM_YceI_1y0gD02 (D:24-188)
1c: PFAM_YceI_1y0gD03 (D:24-188)
1d: PFAM_YceI_1y0gD04 (D:24-188)
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Clan
:
no clan defined [family: YceI]
(5)
Family
:
YceI
(5)
Escherichia coli (strain K12)
(1)
1a
YceI-1y0gD01
D:24-188
1b
YceI-1y0gD02
D:24-188
1c
YceI-1y0gD03
D:24-188
1d
YceI-1y0gD04
D:24-188
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (123 KB)
Header - Asym.Unit
Biol.Unit 1 (60 KB)
Header - Biol.Unit 1
Biol.Unit 2 (60 KB)
Header - Biol.Unit 2
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